2.8 Gene family expansion and contraction
CAFE (version 3.1) (Hahn et al., 2007) was used to analyze gene family expansion and contraction by comparing the S. chinensis genome with those from eight other aphid species (namely D. vitifoliae ,S. flava, E. lanigerum, Ap. glycines, R. maidis, Ac. pisum, D. noxia and M. persicae ). Briefly, the quantitative information of gene families of 10 insects was obtained based on the OrthoMCL results. The number of gene families in each species and the trees with divergence time were used as the input information of CAFE (parameters set to “lambda -s, -t”). The best rates for gene birth and death were decided using CAFE, and all branches had the same rates of gene birth and death. Expansion and contraction of gene families were identified using CAFE (Hahn, Demuth & Han, 2007). GO and KEGG enrichment analyses were conducted using Omicshare CloudTools under default instructions settings (http://www.omicshare.com/).